Align glucose transporter, ATPase component (characterized)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__MR1:202699 Length = 376 Score = 100 bits (249), Expect = 4e-26 Identities = 64/220 (29%), Positives = 119/220 (54%), Gaps = 11/220 (5%) Query: 16 VEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVN 75 + + +IS FG +A+ +++D+ GE++GLLG +G+GK+TL+++++G D+G I Sbjct: 3 IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIHFG 62 Query: 76 GDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECRK 135 V + RD R + ++Q AL ++ A N+ G E++ + ++ Sbjct: 63 NRDVTQVHVRDRR---VGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSH 119 Query: 136 I--MNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVA 193 + M +L Q++ E LSGGQ+Q +A+ARA+ ++L++DEP AL + + Sbjct: 120 LLEMVQLGHLAQRYPE---QLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELR 176 Query: 194 ELIQQL--KAQGIGIFLIDHDVNAVMELCDRASVMKNGQL 231 ++ L + + +F + HD + +EL DR VM NG + Sbjct: 177 RWLRSLHDELKFTSVF-VTHDQDEALELSDRVVVMSNGNI 215 Lambda K H 0.317 0.135 0.373 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 197 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 260 Length of database: 376 Length adjustment: 27 Effective length of query: 233 Effective length of database: 349 Effective search space: 81317 Effective search space used: 81317 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory